If you say the stem has to be the stem of the infinitive, then yes, you'll find lots of irregular verbs. But there's a much better rule, and I'd say the few verbs that don't follow it could be called irregular in the Subjonctif Présent.
- je/tu/il/elle/on/ils/elles: the stem is the Indicatif Présent third person plural, minus -ent
- nous/vous: the stem is the Indicatif Présent second/third first plural, minus -ons
aimer -> ils aiment -> aim-
venir -> ils viennent -> vienn-
tenir -> ils tiennent -> tienn-
prendre -> ils prennent -> prenn-
There are not that many exceptions to this rule. Some important ones:
NOTE: where there are two stems, the second one is for nous/vous, the first one is for all others.
The rule for forming the subjunctive present is just that: take the stem of the third person plural in present tense and add the corresponding subjunctive suffixes.
I agree with you, that they are not really irregular in the way they form the subjunctive. They only are irregular in forming the 3rd person plural, but that's a different matter.
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